User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.4k
Reputation:
1,420
Status:
Trusted
Location:
Italy
Twitter:
@jotsetung
Last seen:
5 days, 3 hours ago
Joined:
4 years, 7 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 266 results • page 1 of 27 • next >
1
vote
1
answer
46
views
1
answers
Answer: A: Gene biotype for a given symbol
... You can get that information using `ensembldb`: Assuming you're working with human annotations and want to use Ensembl release 86: ``` library(EnsDb.Hsapiens.v86) edb <- EnsDb.Hsapiens.v86 ## Get the transcript biotype for the gene SMC4 genes(edb, filter = ~ symbol == "SMC4", return.type = "Da ...
written 6 days ago by Johannes Rainer1.4k
1
vote
1
answer
158
views
1
answers
Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Just a small comment to James' excellent answer: if your alignment/gene annotations were based on a specific Ensembl release, you should also ensure that you are loading/adding annotations from the same release. Example, your object is based on Ensembl release 91 data, then you would want to get the ...
written 10 weeks ago by Johannes Rainer1.4k
0
votes
0
answers
77
views
0
answers
Comment: C: mzR unable to open uncorrupted mzXML file
... Before digging into the error message I would make sure that you have all the most recent package versions and that all files are really there. So, please run `BiocManager::install()` to update potentially outdated packages and then `all(file.exists(files))`. You say you have ~ 1500 files, so mayb ...
written 11 weeks ago by Johannes Rainer1.4k
0
votes
0
answers
132
views
0
answers
Job: Postdoctoral researcher in Computational Metabolomics
... Dear all, Eurac Research is looking for a ## Postdoctoral researcher in Computational Metabolomics The Institute for Biomedicine is seeking a highly motivated researcher to join the Computational Metabolomics team. The Institute for Biomedicine is home to an international and interdisciplinary te ...
metabolomics xcms job written 3 months ago by Johannes Rainer1.4k
0
votes
1
answer
174
views
1
answers
Comment: C: How to use EnsDb in annotatePeak from package "ChIPseeker"
... `intronsByTranscript` is exported in ensembldb version 2.6.6 which will be available in a few days. ...
written 3 months ago by Johannes Rainer1.4k
2
votes
1
answer
174
views
1
answers
Answer: A: How to use EnsDb in annotatePeak from package "ChIPseeker"
... The reason is that `ensembldb` doesn't have an `intronsByTranscript` method. I'll add that and it *should* work. cheers, jo ...
written 3 months ago by Johannes Rainer1.4k
1
vote
1
answer
216
views
1
answers
Answer: A: Retrieve canonical transcript for each gene via ensembldb R package
... At present I am not including this information to the ensembldb databases. So there is no way to get the canonical transcript for a gene using ensembldb. Sorry for that. ...
written 4 months ago by Johannes Rainer1.4k
0
votes
2
answers
165
views
2
answers
Comment: C: Troubles with mzR and BiocInstaller
... Also, the message is rather a warning than an error. mzR will most likely work as expected.   ...
written 5 months ago by Johannes Rainer1.4k
1
vote
0
answers
161
views
0
answers
Comment: C: make TxDb from list of genes
... I agree with James. No need to create a new TxDb database. You could simply subset an EnsDb database to your list of input genes (even better if you have Ensembl IDs): assuming you have your Ensembl gene IDs in a variable called ensids: library(EnsDb.Hsapiens.v86) edb <- filter(EnsDb.Hsapiens.v ...
written 6 months ago by Johannes Rainer1.4k
0
votes
1
answer
167
views
1
answers
Answer: A: Pick coding vs non-coding from Ensembl data set
... You can simply filter the complete EnsDb database to contain only protein coding genes or all other genes (note: this includes miRNA genes, lincRNAs, pseudogenes, snoRNA, scaRNA, sRNA, scRNA, rRNA ...). > library(EnsDb.Hsapiens.v86) > ## Filter the EnsDb database for protein coding genes > ...
written 6 months ago by Johannes Rainer1.4k

Latest awards to Johannes Rainer

Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 5 months ago, created an answer that has been accepted. For A: Ensembl plants at annotationHub?
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve canonical transcript for each gene via ensembldb R package
Popular Question 7 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 7 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 7 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 8 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 9 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 12 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 12 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 24 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 24 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 24 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 24 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 24 months ago, received more than 100 upvotes.
Voter 24 months ago, voted more than 100 times.
Scholar 24 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 24 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 24 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 24 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Scholar 2.0 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 2.0 years ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 125 users visited in the last hour